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New JIRA instance broken Confluence links

Edited

Hi,
We recently migrated our software projects into 1 JIRA system which already hosted Service Desk.

The links for Software projects in Confluence are suffering. I tried to do the following: https://confluence.atlassian.com/confkb/how-to-bulk-update-jira-issue-macro-to-point-to-a-different-jira-instance-596771463.html

Funny thing is that it worked perfectly in the clone to test, but sporadically worked in our prod instance. 

Has anyone else struggled with this?

 

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